Nasopharyngeal colonization by Streptococcus pneumoniae and other common bacteria eight years following introduction of pneumococcal conjugate vaccine in rural South African children ≤5 years old.

Streptococcus pneumoniae remains a leading cause of morbidity and mortality in children Acinetobacter baumannii (36.8% vs 1.1%, aOR:50.11, 95%CI:23.14-108.50), Klebsiella pneumoniae (13.2% vs 0.6%, aOR:22.16, 95%CI:8.03-61.11), Streptococcus pyogenes (2.5% vs 0.2%, aOR:14.49, 95%CI:1.89-111.09) and Neisseria lactamica (8.1% vs 4%, aOR:2.14, 95%CI:1.28-3.57), whereas Streptococcus oralis (0.5% vs 2.2%, aOR:0.21, 95%CI:0.06-0.77) and Moraxella catarrhalis (60.4% vs 67.8%, aOR:0.72, 95%CI:0.56-0.91) were lower. There was an 80% lower prevalence of PCV13-VT serotype colonisation after eight years of routine PCV immunisation, however, there was high residual prevalence of 19F and 6B, serotypes that also persist in disease. The clinical relevance of temporal changes in colonization by other bacteria warrant further investigation.